miRNAsong: a web-based tool for generation and testing of miRNA
sponge constructs in silico

J 2016

miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico

BÁRTA, Tomáš, Lucie PEŠKOVÁ a Aleš HAMPL

Základní údaje

Originální název

miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico

Autoři

BÁRTA, Tomáš (203 Česká republika, garant, domácí), Lucie PEŠKOVÁ (203 Česká republika, domácí) a Aleš HAMPL (203 Česká republika, domácí)

Vydání

Scientific Reports, London, Nature Publishing Group, 2016, 2045-2322

Další údaje

Jazyk

angličtina

Typ výsledku

Článek v odborném periodiku

Obor

Genetika a molekulární biologie

Stát vydavatele

Velká Británie a Severní Irsko

Utajení

není předmětem státního či obchodního tajemství

Impakt faktor

Impact factor: 4.259

Kód RIV

RIV/00216224:14110/16:00088493

Organizační jednotka

Lékařská fakulta

DOI

http://dx.doi.org/10.1038/srep36625

UT WoS

000388072000001

Klíčová slova anglicky

MICRORNA TARGET RECOGNITION; EMBRYONIC STEM-CELLS; CUMATE GENE-SWITCH; MAMMALIAN-CELLS; C-MYC; LENTIVIRAL VECTORS; MIR-145; CANCER; EXPRESSION; PREDICTION

Štítky

EL OK

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 2. 1. 2017 09:35, Ing. Mgr. Věra Pospíšilíková

Anotace

V originále

MicroRNA (miRNA) sponges are RNA transcripts containing multiple high-affinity binding sites that associate with and sequester specific miRNAs to prevent them from interacting with their target messenger (m) RNAs. Due to the high specificity of miRNA sponges and strong inhibition of target miRNAs, these molecules have become increasingly applied in miRNA loss-of-function studies. However, improperly designed sponge constructs may sequester off-target miRNAs; thus, it has become increasingly important to develop a tool for miRNA sponge construct design and testing. In this study, we introduce microRNA sponge generator and tester (miRNAsong), a freely available web-based tool for generation and in silico testing of miRNA sponges. This tool generates miRNA sponge constructs for specific miRNAs and miRNA families/clusters and tests them for potential binding to miRNAs in selected organisms. Currently, miRNAsong allows for testing of sponge constructs in 219 species covering 35,828 miRNA sequences. Furthermore, we also provide an example, supplemented with experimental data, of how to use this tool. Using miRNAsong, we designed and tested a sponge for miR-145 inhibition, and cloned the sequence into an inducible lentiviral vector. We found that established cell lines expressing miR-145 sponge strongly inhibited miR-145, thus demonstrating the usability of miRNAsong tool for sponge generation.

Návaznosti

GJ16-24004Y, projekt VaV

Název: Indukce buněčné plasticity prostřednictvím modulace mikroRNA molekul: Nový přístup pro přeprogramování buněk

Investor: Grantová agentura ČR, Indukce buněčné plasticity prostřednictvím modulace mikroRNA molekul: Nový přístup pro přeprogramování buněk

MUNI/A/1352/2015, interní kód MU

Název: Zdroje pro tkáňové inženýrství 6 (Akronym: TissueENG 6)

Investor: Masarykova univerzita, Zdroje pro tkáňové inženýrství 6, DO R. 2020_Kategorie A - Specifický výzkum - Studentské výzkumné projekty

Citovat

BÁRTA, Tomáš, Lucie PEŠKOVÁ a Aleš HAMPL. miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico. Scientific Reports. London: Nature Publishing Group, 2016, roč. 6, "neuvedeno", s. 1-8. ISSN 2045-2322. Dostupné z: https://dx.doi.org/10.1038/srep36625.

@article{1366170,
   author = {Bárta, Tomáš and Pešková, Lucie and Hampl, Aleš},
   article_location = {London},
   article_number = {"neuvedeno"},
   doi = {http://dx.doi.org/10.1038/srep36625},
   keywords = {MICRORNA TARGET RECOGNITION; EMBRYONIC STEM-CELLS; CUMATE GENE-SWITCH; MAMMALIAN-CELLS; C-MYC; LENTIVIRAL VECTORS; MIR-145; CANCER; EXPRESSION; PREDICTION},
   language = {eng},
   issn = {2045-2322},
   journal = {Scientific Reports},
   title = {miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico},
   volume = {6},
   year = {2016}
}

TY  - JOUR
ID  - 1366170
AU  - Bárta, Tomáš - Pešková, Lucie - Hampl, Aleš
PY  - 2016
TI  - miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico
JF  - Scientific Reports
VL  - 6
IS  - "neuvedeno"
SP  - 1-8
EP  - 1-8
PB  - Nature Publishing Group
SN  - 20452322
KW  - MICRORNA TARGET RECOGNITION
KW  - EMBRYONIC STEM-CELLS
KW  - CUMATE GENE-SWITCH
KW  - MAMMALIAN-CELLS
KW  - C-MYC
KW  - LENTIVIRAL VECTORS
KW  - MIR-145
KW  - CANCER
KW  - EXPRESSION
KW  - PREDICTION
N2  - MicroRNA (miRNA) sponges are RNA transcripts containing multiple high-affinity binding sites that associate with and sequester specific miRNAs to prevent them from interacting with their target messenger (m) RNAs. Due to the high specificity of miRNA sponges and strong inhibition of target miRNAs, these molecules have become increasingly applied in miRNA loss-of-function studies. However, improperly designed sponge constructs may sequester off-target miRNAs; thus, it has become increasingly important to develop a tool for miRNA sponge construct design and testing. In this study, we introduce microRNA sponge generator and tester (miRNAsong), a freely available web-based tool for generation and in silico testing of miRNA sponges. This tool generates miRNA sponge constructs for specific miRNAs and miRNA families/clusters and tests them for potential binding to miRNAs in selected organisms. Currently, miRNAsong allows for testing of sponge constructs in 219 species covering 35,828 miRNA sequences. Furthermore, we also provide an example, supplemented with experimental data, of how to use this tool. Using miRNAsong, we designed and tested a sponge for miR-145 inhibition, and cloned the sequence into an inducible lentiviral vector. We found that established cell lines expressing miR-145 sponge strongly inhibited miR-145, thus demonstrating the usability of miRNAsong tool for sponge generation.
ER  -

BÁRTA, Tomáš, Lucie PEŠKOVÁ a Aleš HAMPL. miRNAsong: a web-based tool for generation and testing of miRNA sponge constructs in silico. \textit{Scientific Reports}. London: Nature Publishing Group, 2016, roč.~6, ''neuvedeno'', s.~1-8. ISSN~2045-2322. Dostupné z: https://dx.doi.org/10.1038/srep36625.

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